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Data

The Epigenomics program and our associated groups generate more than 1,000 genome-wide epigenomic datasets every year. Where appropriate, experiments have been deposited to the NCBI GEO or dbGap databases.

Below are links to the most frequently used datasets to which the Broad Epigenomics Program has contributed. To request data not listed here, contact Liz Gaskell.

 

Epigenomics community projects

BLUEPRINT Epigenome
International Human Epigenome Consortium (IHEC)
Encyclopedia of DNA Elements (ENCODE)
Human Body Map lincRNA
NIH Roadmap Epigenomics Project
Browser | Table

 

 

Data from individual studies

Publication Access link
Liau BB, Sievers C, et al. Adaptive chromatin remodeling drives glioblastoma stem cell plasticity and drug tolerance. Cell Stem Cell. 2017.

GSE74557

Tirosh I, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016. GSE70630
Drier Y, et al. An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nat Genet. 2016. GSE76465
Flavahan WA, Drier Y, et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2016. GSE70991
van Galen P, et al. A multiplexed system for quantitative comparisons of chromatin landscapes. Mol Cell. 2016.  GSE74359
Ryan RJH, et al. Detection of enhancer-associated rearrangements reveals mechanisms of oncogene dysregulation in B-cell lymphoma. Cancer Discov. 2015. GSE69558
Liao J, Karnik R, et al. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet. 2015. GSE63281
Ziller MJ, Edri R, et al. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 2015. GSE62193
Tsankov AM, et al. Transcription factor binding dynamics during human ES cell differentiation. Nature. 2015. GSE61475
Farh KKH, et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015. Portal
Patel AP, Tirosh I, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014. GSE57872
Landau DA, et al. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell. 2014. GSE58889
Smith ZD, Chan MM, Humm KC, et al. DNA methylation dynamics of the human preimplantation embryo. Nature. 2014. GSE51239
Zhu J, et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013. Portal
Ziller MJ, et al. Charting a dynamic DNA methylation landscape of the human genome. Nature. 2013. GSE46644
Smith ZD, et al. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature. 2012. GSE34864
Ram O, Goren A, et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011. Portal
Ernst J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011. Portal (Broad) and Portal (MIT)
Wang H, Zou J, et al. Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proc Natl Acad Sci U S A. 2011. GSE29544
Mikkelsen TS, et al. Dissecting direct reprogramming through integrative genomic analysis. Nature. 2008. GSE11074
Ku M, Koche RP, Rheinbay E, et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 2008. GSE13084
Meissner A, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008. GSE11034 GSE11172 GSE11483 processed data is archived here)
Mikkelsen TS, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007. GSE12241 (processed data is archived here)
Goren A, Ozsolak F, Shoresh N, Ku M, et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010. GSE12241 (processed data is archived here)
Older processed data is archived here.